MolNFT v1 · #169417 · protein
Crystal structure of azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with 3-hydroxypropionic acid
6XB9 · Cysteine dioxygenase type I protein: “Crystal structure of azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with…”. X-ray diffraction, 4 ligands (3OH, FE, MG), 19 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6XB9
- Type
- protein
- Length
- 2,303 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine dioxygenase type I protein
- UniProt
- C1DN94
- Ligands
- 3OH, FE, MG, CL
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, H, J | Cysteine dioxygenase type I protein | protein | 194 | 21% helix, 35% strand | C1DN94 |
| B, D, E, K | Cysteine dioxygenase type I protein | protein | 193 | 21% helix, 36% strand | C1DN94 |
| C | Cysteine dioxygenase type I protein | protein | 193 | 19% helix, 35% strand | C1DN94 |
| F | Cysteine dioxygenase type I protein | protein | 187 | 21% helix, 35% strand | C1DN94 |
| I | Cysteine dioxygenase type I protein | protein | 189 | 20% helix, 37% strand | C1DN94 |
| L | Cysteine dioxygenase type I protein | protein | 186 | 20% helix, 36% strand | C1DN94 |
Ligands and binding sites
- 3OH · 3-hydroxy-propanoic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, H, J
- CL · Chloride ion · ion · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.78 | 0.81 | 96 | empty |
| 2 | 607 | 0.62 | 0.74 | 61 | empty |
| 3 | 489 | 0.62 | 0.75 | 43 | empty |
| 4 | 304 | 0.59 | 0.78 | 43 | empty |
| 5 | 320 | 0.58 | 0.77 | 50 | empty |
Interfaces
17 interfaces between chains.
- B–G · 1381 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1346 Ų buried · 23 hydrogen bonds · protein-protein
- I–K · 1265 Ų buried · 25 hydrogen bonds · protein-protein
- J–L · 1240 Ų buried · 25 hydrogen bonds · protein-protein
- F–I · 546 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XB9 · Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C1DN94
- Elsewhere: RCSB PDB 6XB9 · PDBe 6XB9 · UniProt C1DN94
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